On a roll : a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
© 2023. The Author(s)..
OBJECTIVE: Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and compared three DNA extraction approaches (water filtration, roller trimming and direct buffer) using two different platforms (Qiacube, Kingfisher). DNA extraction methods were evaluated based on cost, effort, DNA concentration and PCR result.
RESULTS: The roller trim method emerged as the optimal method with the best PCR results, DNA concentration and cost efficiency, while the buffer-based methods were the least labour intensive but produced mediocre PCR results and DNA concentrations. Additionally, the Kingfisher magnetic bead extractions generally ranked higher in all categories over the Qiacube column-based DNA extractions. Ultimately, the ideal DNA extraction method for a particular study is influenced by logistical constraints in the field such as the size of the roller, the availability of cold storage, and time constraints on the project. Our results demonstrate the strengths and weaknesses of each approach, allowing for informed decision making by researchers.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:16 |
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| Enthalten in: |
BMC research notes - 16(2023), 1 vom: 18. Dez., Seite 370 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Guthrie, Austin M [VerfasserIn] |
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| Links: |
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| Themen: |
059QF0KO0R |
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| Anmerkungen: |
Date Completed 20.12.2023 Date Revised 21.12.2023 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s13104-023-06669-5 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM366017144 |
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| 100 | 1 | |a Guthrie, Austin M |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a On a roll |b a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces |
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| 500 | |a Date Revised 21.12.2023 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2023. The Author(s). | ||
| 520 | |a OBJECTIVE: Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and compared three DNA extraction approaches (water filtration, roller trimming and direct buffer) using two different platforms (Qiacube, Kingfisher). DNA extraction methods were evaluated based on cost, effort, DNA concentration and PCR result | ||
| 520 | |a RESULTS: The roller trim method emerged as the optimal method with the best PCR results, DNA concentration and cost efficiency, while the buffer-based methods were the least labour intensive but produced mediocre PCR results and DNA concentrations. Additionally, the Kingfisher magnetic bead extractions generally ranked higher in all categories over the Qiacube column-based DNA extractions. Ultimately, the ideal DNA extraction method for a particular study is influenced by logistical constraints in the field such as the size of the roller, the availability of cold storage, and time constraints on the project. Our results demonstrate the strengths and weaknesses of each approach, allowing for informed decision making by researchers | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a DNA extraction | |
| 650 | 4 | |a Environmental DNA | |
| 650 | 4 | |a eDNA | |
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| 700 | 1 | |a Cooper, Christine E |e verfasserin |4 aut | |
| 700 | 1 | |a Bateman, Philip W |e verfasserin |4 aut | |
| 700 | 1 | |a van der Heyde, Mieke |e verfasserin |4 aut | |
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